fix some more iv depwarns and slap a downstream test on

Author: ChrisRackauckas

.github/workflows/Downstream.yml

@@ -0,0 +1,50 @@
+name: IntegrationTest
+on:
+  push:
+    branches: [master]
+    tags: [v*]
+  pull_request:
+
+jobs:
+  test:
+    name: ${{ matrix.package.repo }}/${{ matrix.package.group }}
+    runs-on: ${{ matrix.os }}
+    env:
+      GROUP: ${{ matrix.package.group }}
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version: [1]
+        os: [ubuntu-latest]
+        package:
+          - {user: SciML, repo: Catalyst.jl, group: All}
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: x64
+      - uses: julia-actions/julia-buildpkg@latest
+      - name: Clone Downstream
+        uses: actions/checkout@v2
+        with:
+          repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
+          path: downstream
+      - name: Load this and run the downstream tests
+        shell: julia --color=yes --project=downstream {0}
+        run: |
+          using Pkg
+          try
+            # force it to use this PR's version of the package
+            Pkg.develop(PackageSpec(path="."))  # resolver may fail with main deps
+            Pkg.update()
+            Pkg.test()  # resolver may fail with test time deps
+          catch err
+            err isa Pkg.Resolve.ResolverError || rethrow()
+            # If we can't resolve that means this is incompatible by SemVer and this is fine
+            # It means we marked this as a breaking change, so we don't need to worry about
+            # Mistakenly introducing a breaking change, as we have intentionally made one
+            @info "Not compatible with this release. No problem." exception=err
+            exit(0)  # Exit immediately, as a success
+          end

src/systems/diffeqs/abstractodesystem.jl

@@ -6,7 +6,7 @@ function calculate_tgrad(sys::AbstractODESystem;
   # have `u(t) * t` we want to have the tgrad to be `u(t)` instead of `u'(t) *
   # t + u(t)`.
   rhs = [detime_dvs(eq.rhs) for eq ∈ equations(sys)]
-  iv = sys.iv
+  iv = get_iv(sys)
   xs = states(sys)
   rule = Dict(map((x, xt) -> xt=>x, detime_dvs.(xs), xs))
   rhs = substitute.(rhs, Ref(rule))
@@ -22,7 +22,7 @@ function calculate_jacobian(sys::AbstractODESystem;
     isempty(sys.jac[]) || return sys.jac[]  # use cached Jacobian, if possible
     rhs = [eq.rhs for eq ∈ equations(sys)]
 
-    iv = sys.iv
+    iv = get_iv(sys)
     dvs = states(sys)
 
     if sparse
@@ -38,13 +38,13 @@ end
 function generate_tgrad(sys::AbstractODESystem, dvs = states(sys), ps = parameters(sys);
                         simplify=false, kwargs...)
     tgrad = calculate_tgrad(sys,simplify=simplify)
-    return build_function(tgrad, dvs, ps, sys.iv; kwargs...)
+    return build_function(tgrad, dvs, ps, get_iv(sys); kwargs...)
 end
 
 function generate_jacobian(sys::AbstractODESystem, dvs = states(sys), ps = parameters(sys);
                            simplify=false, sparse = false, kwargs...)
     jac = calculate_jacobian(sys;simplify=simplify,sparse=sparse)
-    return build_function(jac, dvs, ps, sys.iv; kwargs...)
+    return build_function(jac, dvs, ps, get_iv(sys); kwargs...)
 end
 
 function generate_function(sys::AbstractODESystem, dvs = states(sys), ps = parameters(sys); kwargs...)
@@ -244,7 +244,7 @@ function process_DEProblem(constructor, sys::AbstractODESystem,u0map,parammap;
                            kwargs...)
     dvs = states(sys)
     ps = parameters(sys)
-    u0map′ = lower_mapnames(u0map,sys.iv)
+    u0map′ = lower_mapnames(u0map,get_iv(sys))
     u0 = varmap_to_vars(u0map′,dvs; defaults=default_u0(sys))
 
     if !(parammap isa DiffEqBase.NullParameters)

src/systems/reaction/reactionsystem.jl

@@ -441,7 +441,7 @@ function Base.convert(::Type{<:SDESystem},rs::ReactionSystem, combinatoric_ratel
 
     SDESystem(eqs,
               noiseeqs,
-              get_iv(iv),
+              get_iv(rs),
               states(rs),
               (noise_scaling===nothing) ?
                     get_ps(rs) :